Volume scatter without rendering the volume object
Sorry if I'm not picking up on your situation exactly, but is your atmosphere scatter mesh using a volumetric shaded material?  Is it only shaded by volume, or is there also a surface component?

If it is helpful, and if your volume scatter mesh is volume only, I can tell you how to add a gradient to the volume density.  That means you can make the edges of the volume scatter effect fade out, rather than be abrupt.

Here is a two-sphere setup where the volume scatter sphere does not have the gradient:



Here is the same with the gradient enabled:



Hope this helps!